[Rcpp-devel] Rcpp question regarding compilation of another package

Dirk Eddelbuettel edd at debian.org
Tue Dec 13 14:31:11 CET 2016

Thanks for posting here, and showing complete references. Your earlier
StackOverflow questions went nowhere.  Hopefully we can tackle this here.

On 12 December 2016 at 17:32, khagay nagdimov wrote:
| I am trying to create a package that uses Rcpp to translate code from SeqLib ( 
| https://github.com/walaj/SeqLib) into R. I have compiled SeqLib but, I still
| have problems referencing the function definitions. The current structure of my
| R package is shown here: https://github.com/KhagayN/SeqLibr

A bit of a mess. The repo is full of object files (.o), editor backups (*~),
editor temp files (#*#).  But at least you are using the right editor.

I have no experience with git submodules and cannot say wether SeqLib again
in SeqLibR is a good idea.
| My makevars links to the location of the header files and to the static
| libraries. To my understanding, the header files linked via PKG_CXXFLAGS point
| to the header files and PKG_LIBS points to the static libraries. Then, in

The Makevars is suspicious:

    ## the following flags are for PreProcessor.
    PKG_CPPFLAGS= -I../bwa/ -I../ -I../src/SeqLib/* 

First, the ../bwa/ directory does not work.  R includes _everything below
inst/_ but only a few known directories at the top-level.  This is why we all
put headers into inst/include/ --- so I would make **very strongly** suggest
you move bwa/ into inst/include/bwa and then use -I../inst/include/bwa.

Second, you are in src/ so ../src/ makes no sense. Make that -ISeqLib/

Third, there is no notion of wildcards in include directories.  So -ISeqLib/

Fourth, for SeqLib you do

   ( cd SeqLib; ./configure; make; make install; )

and you _almost surely_ should not run 'make install'.  The rest of your
src/Makevars is trying to use the static library from that directory; make
install would attempt to write the library somewhere else.  "Writing R
Extensions* _explicitly_ prohibits that for good reason.

I stop here.  Other failures related to loading object are likely due to
these issues which you probably want to correct first.


| rcpp_hello_world.cpp, I reference a function called Open within the FastqReader
| class within the SeqLib namespace but, when I run load_all() I get an effor
| saying:
| Error in dyn.load(dllfile);
|    unable to load shared object 'subsetSeqLib.so': undefined symbol:
| _ZN6SeqLib11FastqReader40OpenERKSs, which references that Open function from
| FastqReader. I don't understand why this is happening since I am linked to the
| static libraries that have the definition of that function.
| Thanks for all the help. 
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http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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